First, he points that -- contrary to what scientists used to believe -- there may be no "threshold" where the effects of altitude start to slow you down. Instead, for at least some people, VO2max may start to decline pretty much as soon as you climb above sea level. He cites a 2006 European Journal of Applied Physiology study from Norwegian researchers that found a linear decline in VO2max between 300 and 2800 meters above sea level; here's what that data looked like (top graph shows average, bottom graphs shows individual subjects):

The primary point that Chapman makes in his paper is that not everyone responds in the same way to altitude. For one thing, trained athletes with high VO2max are likely to suffer a larger decline (both in absolute and percentage terms) than sedentary people when they go to altitude. There are a number of possible reasons for this. For example, trained athletes have powerful hearts that pump a large volume of blood with each stroke. That means that during exercise (when the heart is beating most quickly), blood is rushing past the lungs so quickly that it may not have a chance to pick up a full load of oxygen. The result is "exercise-induced arterial hypoxemia," (EIAH) a lowering of oxygen levels in the blood that occurs even at sea level in about half of trained athletes. There are also other causes of EIAH: for example, some people run into mechanical limits on the amount of air they can breathe in and out sooner than others.

It turns out that this EIAH is a crucial predictor of altitude performance. If you hop on a treadmill at sea level and run hard, you may or may not experience a decrease in oxygen levels in your blood. If you do, you're likely to be very sensitive to the effects of altitude. Some sample data that Chapman shows: someone with no EIAH might reach 95% oxygen saturation in the blood during exercise at sea level, and 93% at altitude; some with EIAH might get down to 89% at sea level and 83% at elevation, which is enough to cause a significant decline in VO2max and running performance. Sure enough, when they do studies, they can predict based on blood oxygen levels at sea level who will likely experience the greatest decline in performance at altitude.

So how do you "fix" this? It's not clear at this point, though I've heard some speculation that respiratory muscle training might be one avenue to explore. For now, what may be most useful is the ability to diagnose and predict who will respond well to altitude. Some athletes may be mildly compromised and need to take it really easy for the first week or so of an altitude training camp; others may be heavily compromised and be better off skipping altitude training entirely. That could be useful to know before planning your season around a trip to the mountains (though the scenery may make it worthwhile anyway!).